Basic Concepts in Biochemistry: A Student's Survival
Guide

By: Hiram F. Gilbert

ISBN: 0071356576



ISBN-13: 9780071356572

Publisher: McGraw-Hill Medical - 1999-11-16

Paperback | 2 Edition | 331 Pages











Annotation:

"...reviews the most difficult concepts in biochemistry for maximum
comprehension in a short period of time...emphasizes a mastering of
fundamental concepts, not memorizing facts, so that students truly
comprehend & can apply the material.







From the Publisher:

This second edition continues to innovatively review the toughest
concepts in biochemistry for maximum comprehension in a short period of
time. Unlike conventional texts or review books that stress memorizing
facts, BASIC CONCEPTS stresses the mastering of fundamental concepts, so
that the reader truly comprehends the material and feels comfortable
applying it. Dr. Gilbert uses simple, jargon-free language and
award-winning teaching techniques including algorithms, mnemonics and
clinical examples.



Synopsis:

Do you find biochemistry daunting? If so, this time-saving guide offers
all the help you need. Compact, yet comprehensive, the second edition of
BASIC CONCEPTS IN BIOCHEMISTRY breaks down the complexities of
biochemistry into jargon-free, easy-to-remember steps that show you how
biochemistry works.And unline reviews that emphasize memorization of
facts, this book helps you master the topics that students find most
difficult, building your understanding with explanations in everyday
language. You'll comprehend the material and feel more comfortable
applying it. Along with enhanced figures, the new edition contains two
new chapters - one that outlines the concepts of membranes and membrane
proteins, and another that focuses on signal transduction pathways.
OTHER FEATURES TO LOOK FOR: Building-block format, providing clear
connections between easier and more difficult topics; Empahsis on
concepts - not facts - for a handle on any problem; Summary boxes,
diagrams, and tables that speed review and clarify key points. BASIC
CONCEPTS IN BIOCHEMISTRY has just one goal: to review the toughest
concepts in biochemistry in an accessible format so your understanding
is thorough and complete. Look for these other BASIC CONCEPTS titles:
Cell biology; Embryology; Immunology; Pathology; Pharmacology.





Table of Contents:





Preface xiii

Prologue xv

Chapter 1 Where to Start 1

Instructions 1

What Do I Need to Know? 2

Instructions for Use 2

Studying and Exams 2

Trivia Sorter 4

Chapter 2 Protein Structure 6

Amino Acid Structure 6

Interactions 8

Water 9

Hydrophobic Interaction 9

van der Waals Interactions and London Dispersion Forces 11

Hydrogen Bonds 11

Secondary Structure 12

Protein Stability 15

Favorable (Good) Interactions 17

Unfavorable (Bad) Interactions 17

Temperature-Sensitive Mutations 19

Ligand-Binding Specificity 20

Global Conclusion 21

Chapter 3 Membranes and Membrane Proteins 22

General Membrane Function 22

Membrane Composition 23

Phospholipid Bilayer 24

Membrane Structure 25

Posttranslational Modification 26

Membrane Fluidity 27

Diffusion in Membranes 28

Movement of Ions and Molecules Across Membranes 28

Transport Across Membranes 29

The Nernst Equation 31

Chapter 4 DNA-RNA Structure 35

DNA Structure 35

DNA Stability 37

RNA Secondary Structure 38

Chapter 5 Expression of Genetic Information 40

Information Metabolism 40

Directions and Conventions 41

DNA Replication 42

Types of DNA Polymerase 45

Recombination 47

Regulation of Information Metabolism 49

Transcription 53

Regulation of Transcription 55

Translation 57

Use of High-Energy Phosphate Bonds During Translation 60

Chapter 6 Recombinant-DNA Methodology 61

Restriction Analysis 61

Gels and Electrophoresis 65

Blotting 67

Restriction Fragment-Length Polymorphism 69

Cloning 70

Sequencing 73

Mutagenesis 75

Polymerase Chain Reaction 76

Chapter 7 Enzyme Mechanism 80

Active Site 81

Transition State 81

Catalysis 83

Lock and Key 83

Induced Fit 83

Nonproductive Binding 85

Entropy 87

Strain and Distortion 88

Transition-State Stabilization 88

Transition-State Analogs 91

Chemical Catalysis 93

Chapter 8 Enzyme Kinetics 95

S, P, and E (Substrate, Product, Enzyme) 96

Amounts and Concentrations 96

Active Site 97

Assay 98

Velocity 98

Initial Velocity 100

Mechanism 101

Little k's 102

Michaelis-Menten Equation 103

V[subscript max] 106

K[subscript cat] 106

K[subscript m] 107

Special Points 107

k[subscript cat]/K[subscript m] 107

Rate Accelerations 108

Steady-State Approximation 109

Transformations and Graphs 111

Inhibition 112

Allosterism and Cooperativity 117

The Monod-Wyman-Changeaux Model 119

Chapter 9 Signal Transduction Pathways 123

Signal Transduction Pathways 123

Organization 124

Signals 125

Receptors 126

Soluble Receptors 126

Transmembrane Receptors 128

Enzyme Coupled Receptors 128

G-Protein Coupled Receptors 131

Ion-Channel Coupled Receptors 132

Second Messengers 133

Amplifiers 136

Integrators 137

Inhibitors 138

Chapter 10 Glycolysis and Gluconeogenesis 141

Glycolysis Function 143

Glycolysis Location 143

Glycolysis Connections 143

Glycolysis Regulation 143

Glycolysis ATP Yields 144

Glycolysis Equations 144

Effect of Arsenate 144

Lactate or Pyruvate 145

Gluconeogenesis Function 145

Gluconeogenesis Location 145

Gluconeogenesis Connections 145

Gluconeogenesis Regulation 146

Gluconeogenesis ATP Costs 146

Gluconeogenesis Equations 146

Chapter 11 Glycogen Synthesis and Degradation 147

Function 147

Location 147

Connections 148

Regulation 148

ATP Yield 150

ATP Cost 150

Molecular Features 150

Chapter 12 TCA Cycle 153

TCA Cycle 153

Chapter 13 Fat Synthesis and Degradation 155

Fatty Acid Synthesis Function 156

Fatty Acid Synthesis Location 156

Fatty Acid Synthesis Connections 157

Fatty Acid Synthesis Regulation 157

Fatty Acid Synthesis ATP Costs (for C[subscript 16]) 157

Fatty Acid Synthesis Equation 159

Elongation and Desaturation 160

Triglyceride and Phospholipid Synthesis 162

[beta]-Oxidation Function 164

[beta]-Oxidation Location 164

Carnitine Shuttle 164

[beta]-Oxidation Connections 164

[beta]-Oxidation Regulation 164

[beta]-Oxidation ATP Yield 166

[beta]-Oxidation Equation 167

[beta]-Oxidation of Unsaturated Fatty Acids 168

[beta]-Oxidation of Odd-Chain-Length Fatty Acids 172

Chapter 14 Electron Transport and Oxidative Phosphorylation 173

Oxidation and Reduction 173

The Electron Transport Chain 174

Connections 176

Regulation 178

P/O Ratios 178

Uncouplers 179

Inhibitors 180

Chapter 15 Pentose Phosphate Pathway 183

Pentose Phosphate Pathway 183

Chapter 16 Amino Acid Metabolism 186

Nonessential Amino Acid Synthesis 186

Essential Amino Acids 187

Amino Acid Degradation 187

Generalities of Amino Acid Catabolism 187

Products of Amino Acid Degradation 188

Chapter 17 Integration of Energy Metabolism 190

Integrating Metabolic Pathways 191

ATP 192

Glucose 192

Storage Molecules 193

Metabolic States and Signals 194

Insulin 195

Glucagon 196

Epinephrine 197

Secondary Signals 198

Generalities of Metabolism 199

Phosphorylation 202

Glycogen 204

Metabolic Movements of Glycogen 205

Fat 207

Metabolic Movements of Fat 207

Protein 209

Metabolic Movements of Protein 209

Tissue Cooperation 211

Liver 212

Muscle 212

Adipose 212

Brain 213

Connection of Storage Pools 213

Feeding 214

Fasting 214

Starvation 217

Excitement 219

Interorgan Cycles 221

Cori Cycle 221

Alanine Cycle 222

Ketone Bodies 223

Chapter 18 Urea Cycle 225

Urea Cycle 225

Chapter 19 Purine Metabolism 227

Purine Synthesis 227

Purine Salvage 228

Deoxynucleotides 228

Purine Degradation 229

Chapter 20 Pyrimidine Metabolism 230

Pyrimidine Synthesis 230

Pyrimidine Salvage 231

Pyrimidine Degradation 232

Chapter 21 One-Carbon Metabolism 233

One-Carbon Metabolism 233

Oxidation States of Carbon 233

Chapter 22 Tracking Carbons 236

Glucose to Pyruvate 236

TCA Cycle 238

Chapter 23 ph, pK[subscript A], Problems 241

Proton: H[superscript +] or H[subscript 3]O[superscript +] 242

Acid 242

Base 242

Not All Acids and Bases Are Created Equal 243

pK[subscript a] = -log (K[subscript a]) 244

Weak Acids Make Strong Bases (and Vice Versa) 244

Who Gets the Proton? 245

Don't Forget Stoichiometry 245

The Sadistic Little p 246

Taking log[subscript 10](x) 247

Taking -log[subscript 10](x) 247

pH = -log[subscript 10] [H[superscript +]] 248

pK[subscript a] = - log[subscript 10] (K[subscript a]) 248

Buffers 248

Henderson-Hasselbalch Equation 249

Titration Curves 250

plIsoelectric Point 254

The Bicarbonate Buffer 255

Imbalance in Blood pH 257

Acidosis and Alkalosis 258

Chapter 24 Thermodynamics and Kinetics 261

Thermodynamics 261

Free Energy 263

Adding Free-Energy Changes 268

Coupling Free Energies 268

Thermodynamic Cycles 269

[Delta]G = [Delta]H - T[Delta]S 272

Driving Force 273

Kinetics 275

Velocity 275

Transition State Theory 276

Rate Constants 277

Rate Constants and Mechanism 283

Appendix 284

Glossary 287

Index 319